Verification of RootPPL on the Bird Trees
Viktor Senderov
01 Apri 2021
What I tested?
trees
[1] "Accipitridae" "BC7" "P20b" "TitTyranRest"
num_nodes
[1] 349 179 249 631
depth
[1] 30 14 15 22
- 10,000 and 100,000 particles
- Comparison to Birch results
Models and priors
Models:
[1] "clads2-d-λ" "clads2-d-λμ" "clads2-d-λμασ" "clads2"
[5] "crbd-d-λ" "crbd-d-λμ" "crbd" "birch-clads2"
[9] "birch-crbda"
- Survivorship bias correction for CRBD not implemented in RootPPL
Priors:
floating_t kLambda = 1.0;
floating_t thetaLambda = 1.0;
floating_t epsMin = 0.0;
floating_t epsMax = 1.0;
floating_t kMu = 1.0;
floating_t thetaMu = 0.5;
floating_t a = 1.0;
floating_t b = 0.2;
- ρ as needed.
Accipitridae (10,000)
evaluate_tree(prepare_tree(1))
var R
clads2-d-λ 3.846580000 20
clads2-d-λμ 3.906802895 20
clads2-d-λμασ 1.541363158 20
clads2 0.845051316 20
crbd-d-λ NA 1
crbd-d-λμ 2.209953684 20
crbd 21.409518684 20
birch-clads2 1.016323218 500
birch-crbda 0.006285234 500
num_nodes[1]
[1] 349
depth[1]
[1] 30
Accipitridae (100,000)
evaluate_tree(prepare_tree(1))
var R
clads2-d-λ 0.155141818 11
clads2-d-λμ 0.255706667 15
clads2-d-λμασ 0.114798095 15
clads2 0.237563810 15
crbd-d-λ 1.120966667 15
crbd-d-λμ 0.531878095 15
crbd 4.393652381 15
birch-clads2 1.016323218 500
birch-crbda 0.006285234 500
num_nodes[1]
[1] 349
depth[1]
[1] 30
BC7 (10,000)
evaluate_tree(prepare_tree(2))
var R
clads2-d-λ 3.46137133 4
clads2-d-λμ 1.64821778 20
clads2-d-λμασ 0.65482912 20
clads2 0.14256552 20
crbd-d-λ NA 1
crbd-d-λμ 0.38469721 20
crbd 0.73701499 20
birch-clads2 0.74300808 500
birch-crbda 0.01485966 500
num_nodes[2]
[1] 179
depth[2]
[1] 14
BC7 (100,000)
evaluate_tree(prepare_tree(2))
var R
clads2-d-λ 0.61351217 15
clads2-d-λμ 0.23900492 15
clads2-d-λμασ 0.10269270 15
clads2 0.01260710 15
crbd-d-λ 0.97300421 15
crbd-d-λμ 0.04667570 15
crbd 0.07152555 15
birch-clads2 0.74300808 500
birch-crbda 0.01485966 500
num_nodes[2]
[1] 179
depth[2]
[1] 14
P20b (10,000)
evaluate_tree(prepare_tree(3))
var R
clads2-d-λ 0.37617343 8
clads2-d-λμ 0.52025194 20
clads2-d-λμασ 0.23428645 20
clads2 0.03408383 20
crbd-d-λ NA 1
crbd-d-λμ 0.34765827 20
crbd 6.95280441 20
birch-clads2 0.28441072 500
birch-crbda 0.01570452 500
num_nodes[3]
[1] 249
depth[3]
[1] 15
P20b (100,000)
evaluate_tree(prepare_tree(3))
var R
clads2-d-λ 0.10591389 15
clads2-d-λμ 0.06628198 15
clads2-d-λμασ 0.01713978 15
clads2 0.00157300 15
crbd-d-λ 1.83595795 15
crbd-d-λμ 0.04814338 15
crbd 0.36755270 15
birch-clads2 0.28441072 500
birch-crbda 0.01570452 500
num_nodes[3]
[1] 249
depth[3]
[1] 15
TitTyranRest (10,000)
evaluate_tree(prepare_tree(4))
var R
clads2-d-λ 6.38903864 12
clads2-d-λμ 4.01094211 20
clads2-d-λμασ 3.86897763 20
clads2 0.29798842 20
crbd-d-λ NA 1
crbd-d-λμ 7.68952079 20
crbd 263.97796211 20
birch-clads2 1.74480633 500
birch-crbda 0.03113397 500
num_nodes[4]
[1] 631
depth[4]
[1] 22
TitTyranRest (100,000)
evaluate_tree(prepare_tree(4))
var R
clads2-d-λ 1.29836190 7
clads2-d-λμ 0.40825714 15
clads2-d-λμασ 0.14945714 15
clads2 0.02689524 15
crbd-d-λ 2.14847429 15
crbd-d-λμ 1.14157810 15
crbd 13.64886000 15
birch-clads2 1.74480633 500
birch-crbda 0.03113397 500
num_nodes[4]
[1] 631
depth[4]
[1] 22